Dopplegangers ARE supernatural, but Amara is NOT a doppleganger. She was a human (Tessa's handmaiden and lover to Silas, who was a witch--Tess and Silas BOTH being supernatural creatures as they are witches) who had an immortality spell cast upon her making her a "supernatural creature" afterwards.
Then on top of this immortality spell, once Tessa and The Travellers got a hold of her created a new spell called "The Other Side" and also I guess you could say, "The Anchor" ("The Anchor" being the physical object description for the otherside's existence).
Then Amara was rescued by Silas who had the immortality cure running in his veins. Silas gave her blood and then also let her know that he had taken the cure (and then Amara confirmed that Silas was STILL actively "the cure" or at least the holder of it). At this point Amara drank Silas's blood, wishing to end her immortality...so she could end her life. She was tired of her existence and who can blame her.
Now, if Amara wasn't a human...not only would Amara by killing herself just make things worse (she would, in effect, be EXACTLY like Bonnie) it would've opened a GIGANTIC hole in the writers logic and theories. This is why I appreciate their attention to details like this, because had they missed it, it totally wouldn't have made sense..later on that is.
But, Amara was human. So if she died TWO things would happen: she would pass on to the NORMAL place where all humans and at least some supernatural creatures (witches really and werewolves as they are the ones that would've been around for the most part before the "otherside" became something real) have [assed onto to. Then her death--since she couldn't become a ghost (that is reserved for those that belong to "The Other Side")--the anchor would shatter and break and then, in turn, "The Other Side" would fall. But, we still don't know what exactly happens when that DOES happen. Do they just pass onto the other realm where all others that have died go to? Or is something much worse in store for the world? Will all the supernatural that have died be forced back into the land of the living? Or is there even worse things in store?
Anyway, once Amara had taken the cure (thus taking away her immortality and making her human), the ONLY thing that would make her "still" supernatural is "The Anchor" (as it is a spell...so...supernatural). But as explained her death expells that spell immediatly...and she knew this. So Amara chose to end her life and that is what she did.
But Bonnie was chosen as the new "Anchor" point. Bonnie being a supernatural creature and therefore a ghost who hadn't passed over to "The Other Side" by "touching Amara"--as others have now touched Bonnie (appearantly "nature" must keep you "away" from "the anchor" if it needs you to "do something...like Bonnie; the Universe had a "job" for Bonnie, one that I doubt The Travellers even know of...and it may be their demise)--she was pushed "one foot" into our realm since "The Anchor" is a real object.
But, when Amara died she was no longer the anchor and also a human...she moved on to where we REALLY are supposed to go to. But, Silas got trapped in Tessa's little, twisted, and maniacal plan...and now resides on "The Other Side".
The dopplegangers are "echoes" created by the immortality spell that Silas created and that Amara partake of. BUT, Amara is the ORIGINAL and was ONLY ever a immortal HUMAN. As I said, once she took the cure, she was just a human--she was never a doppleganger (as a doppleganger even by defintion has to do with those that come after the original...). But some think the dopplegangers are nature's way of punishing Tessa for creating this "Other Side", so that she would endlessly watch these dopplegangers fall in love--dribving her mad or making her learn...that she did something foolish, stupid, and...evil.
I think that covers everything.